├── .gitattributes ├── LICENSE ├── README.md ├── _config.yml ├── lammps_input_files ├── BNC.tersoff ├── force.in ├── forces.in ├── onelayer.data └── relax_thermal.in ├── scripts ├── Makefile └── compactify_vels.cpp ├── sdhc ├── SHC_generate.py ├── __init__.py ├── __main__.py ├── __version__.py └── force_calculate.py └── setup.py /.gitattributes: -------------------------------------------------------------------------------- 1 | # Auto detect text files and perform LF normalization 2 | * text=auto 3 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | When I have time I will finish the README.md. 2 | 3 | Most codes are self-explanatory. -------------------------------------------------------------------------------- /_config.yml: -------------------------------------------------------------------------------- 1 | theme: jekyll-theme-slate 2 | title: Welcome to Spectral-decomposition-python-tools homepage！！！ 3 | -------------------------------------------------------------------------------- /lammps_input_files/BNC.tersoff: -------------------------------------------------------------------------------- 1 | # DATE: 2013-03-21 CONTRIBUTOR: Cem Sevik CITATION: Kinaci, Haskins, Sevik and Cagin, Phys Rev B, 86, 115410 (2012) 2 | # Tersoff parameters for B, C, and BN-C hybrid based graphene like nano structures 3 | # multiple entries can be added to this file, LAMMPS reads the ones it needs 4 | 5 | # these entries are in LAMMPS "metal" units: 6 | # A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms 7 | # other quantities are unitless 8 | 9 | # Cem Sevik (csevik at anadolu.edu.tr) takes full blame for this 10 | # file. It specifies B-N, B-C, and N-C interaction parameters 11 | # generated and published by the reseacrh group of Prof. Tahir Cagin. 12 | 13 | # 1. Physical Review B 84, 085409 2011 14 | # Characterization of thermal transport in low-dimensional boron nitride nanostructures, 15 | # 16 | 17 | # 2. Physical Review B 86, 075403 2012 18 | # Influence of disorder on thermal transport properties of boron nitride nanostructures 19 | # 20 | 21 | # 3. Physical Review B 86, 075403 2012, Please see for further information about B-C and N-C parameters 22 | # Thermal conductivity of BN-C nanostructures 23 | # 24 | 25 | # The file also specifies C-C, interaction parameters 26 | # generated and published by the reseacrh group of Dr. D. A. Broido 27 | # Physical Review B 81, 205441 2010 28 | # Optimized Tersoff and Brenner empirical potential parameters for 29 | # lattice dynamics and phonon thermal transport in carbon nanotubes and graphene 30 | 31 | # Users in referring the full parameters can cite the full parameter paper (3) as: 32 | # A. Kinaci, J. B. Haskins, C. Sevik, T. Cagin, Physical Review B 86, 115410 (2012) 33 | # Thermal conductivity of BN-C nanostructures 34 | # 35 | 36 | # format of a single entry (one or more lines): 37 | # element 1, element 2, element 3, 38 | # m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A 39 | 40 | N B B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 41 | N B N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 42 | N B C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 43 | 44 | B N B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 45 | B N N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 46 | B N C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 47 | 48 | N N B 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866 49 | N N N 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866 50 | N N C 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866 51 | 52 | B B B 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156 53 | B B N 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156 54 | B B C 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156 55 | 56 | C C C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6 57 | C C B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6 58 | C C N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6 59 | 60 | C B B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 61 | C B N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 62 | C B C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 63 | 64 | C N B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 65 | C N N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 66 | C N C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 67 | 68 | B C C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 69 | B C B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 70 | B C N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 71 | 72 | N C C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 73 | N C B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 74 | N C N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 75 | -------------------------------------------------------------------------------- /lammps_input_files/force.in: -------------------------------------------------------------------------------- 1 | ## ***************** Initialization # basis *************** 2 | units metal 3 | dimension 3 4 | boundary p p p 5 | atom_style atomic 6 | 7 | # ****************** Read restart file ***************** 8 | 9 | read_restart optimize.restart # The statement "atom_modify map hash" must be added to the 'in file' that generates the restart file 10 | 11 | # mass 12 | # First layer 13 | 14 | mass 1 10.811000 # B1 15 | mass 2 12.010700 # C1 16 | mass 3 14.006700 # N1 17 | 18 | # ******************* Define a few parameters ********************** 19 | 20 | variable T equal 300 # Average temperature 300K 21 | variable DT equal 0.0005 # Timestep 0.5fs (Read from the restart file) 22 | 23 | # ******************* Fix some atoms to avoid drift ****************** 24 | 25 | variable filetowrite string Fij.dat # For generating the force constant 26 | 27 | # ********************* Potential function setting ***************** 28 | 29 | pair_style tersoff 30 | pair_coeff * * BNC.tersoff B C N 31 | 32 | timestep ${DT} 33 | 34 | # ************************* The following to divide block *********************** 35 | # ************************* For Y direction ************************************** 36 | 37 | variable y_max equal ly 38 | variable P equal ${y_max}/2-100 39 | variable P1 equal ${y_max}/2+100 40 | 41 | variable tmp1 equal ${P1}-${P} 42 | variable tmp equal ${tmp1}/40 43 | variable middle equal ${y_max}/2 44 | 45 | variable L1 equal ${P}+3*${tmp} 46 | variable R1 equal ${P1}-3*${tmp} 47 | 48 | region lfixed block INF INF INF ${P} INF INF units box 49 | region rfixed block INF INF ${P1} INF INF INF units box 50 | 51 | region hot block INF INF ${P} ${L1} INF INF units box 52 | region cold block INF INF ${R1} ${P1} INF INF units box 53 | 54 | region fixed union 2 lfixed rfixed 55 | 56 | region main block INF INF ${P} ${P1} INF INF units box 57 | 58 | region main_nvt block INF INF ${L1} ${R1} INF INF units box 59 | 60 | 61 | group lfixed region lfixed 62 | group rfixed region rfixed 63 | group hot region hot 64 | group cold region cold 65 | 66 | group main region main 67 | group main_nvt region main_nvt 68 | 69 | ## ***************** Frozen atomic group ************** 70 | 71 | group freeze region fixed 72 | 73 | ##***************** Velocity groups for transmission calculation ***************** 74 | 75 | variable dmid equal 6 ## Set to 6 (A) here 76 | variable mid_left equal ${middle}-${dmid} 77 | variable mid_right equal ${middle}+${dmid} 78 | 79 | region int_L block INF INF ${mid_left} ${middle} INF INF units box 80 | region int_R block INF INF ${middle} ${mid_right} INF INF units box 81 | 82 | group interface_L region int_L 83 | group interface_R region int_R 84 | group interface union interface_L interface_R 85 | 86 | ## ************** Freeze (Freeze some of the atoms of the model) ************** 87 | 88 | velocity freeze set 0.0 0.0 0.0 units box 89 | fix 3 freeze nve/noforce 90 | 91 | ## *************** Calculate some thermodymanic quantities ******************* 92 | 93 | compute fxfyfz interface property/atom fx fy fz 94 | compute fxs interface property/atom fx 95 | compute fys interface property/atom fy 96 | compute fzs interface property/atom fz 97 | 98 | ## **************** Sampling data and run 0 ***************** 99 | 100 | fix 1 main nve 101 | 102 | variable N equal "count(all)" 103 | variable NL equal "count(interface_L)" 104 | variable NR equal "count(interface_R)" 105 | 106 | print "NL ${NL}" 107 | print "NR ${NR}" 108 | 109 | -------------------------------------------------------------------------------- /lammps_input_files/forces.in: -------------------------------------------------------------------------------- 1 | ## ***************** Initialization # basis *************** 2 | units metal 3 | dimension 3 4 | boundary p p p 5 | atom_style atomic 6 | atom_modify map hash 7 | 8 | # ****************** Read restart file ***************** 9 | 10 | read_restart optimize.restart # The statement "atom_modify map hash" must be added to the 'in file' that generates the restart file 11 | 12 | # mass 13 | # First layer 14 | 15 | mass 1 10.811000 # B1 16 | mass 2 12.010700 # C1 17 | mass 3 14.006700 # N1 18 | 19 | # ******************* Define a few parameters ********************** 20 | 21 | variable T equal 300 # Average temperature 300K 22 | variable DT equal 0.0005 # Timestep 0.5fs (Read from the restart file) 23 | 24 | # ******************* Fix some atoms to avoid drift ****************** 25 | 26 | variable filetowrite string Fij.dat # For generating the force constant 27 | 28 | # ********************* Potential function setting ***************** 29 | 30 | pair_style tersoff 31 | pair_coeff * * BNC.tersoff B C N 32 | 33 | timestep ${DT} 34 | 35 | # ************************* The following to divide block *********************** 36 | # ************************* For Y direction ************************************** 37 | 38 | variable y_max equal ly 39 | variable P equal ${y_max}/2-100 40 | variable P1 equal ${y_max}/2+100 41 | 42 | variable tmp1 equal ${P1}-${P} 43 | variable tmp equal ${tmp1}/40 44 | variable middle equal ${y_max}/2 45 | 46 | variable L1 equal ${P}+3*${tmp} 47 | variable R1 equal ${P1}-3*${tmp} 48 | 49 | region lfixed block INF INF INF ${P} INF INF units box 50 | region rfixed block INF INF ${P1} INF INF INF units box 51 | 52 | region hot block INF INF ${P} ${L1} INF INF units box 53 | region cold block INF INF ${R1} ${P1} INF INF units box 54 | 55 | region fixed union 2 lfixed rfixed 56 | 57 | region main block INF INF ${P} ${P1} INF INF units box 58 | 59 | region main_nvt block INF INF ${L1} ${R1} INF INF units box 60 | 61 | 62 | group lfixed region lfixed 63 | group rfixed region rfixed 64 | group hot region hot 65 | group cold region cold 66 | 67 | group main region main 68 | group main_nvt region main_nvt 69 | 70 | ## ***************** Frozen atomic group ************** 71 | 72 | group freeze region fixed 73 | 74 | ##***************** Velocity groups for transmission calculation ***************** 75 | 76 | variable dmid equal 6 ## Set to 6 (A) here 77 | variable mid_left equal ${middle}-${dmid} 78 | variable mid_right equal ${middle}+${dmid} 79 | 80 | region int_L block INF INF ${mid_left} ${middle} INF INF units box 81 | region int_R block INF INF ${middle} ${mid_right} INF INF units box 82 | 83 | group interface_L region int_L 84 | group interface_R region int_R 85 | group interface union interface_L interface_R 86 | 87 | ## ************** Freeze (Freeze some of the atoms of the model) ************** 88 | 89 | velocity freeze set 0.0 0.0 0.0 units box 90 | fix 3 freeze nve/noforce 91 | 92 | ## *************** Calculate some thermodymanic quantities ******************* 93 | 94 | compute fxfyfz interface property/atom fx fy fz 95 | compute fxs interface property/atom fx 96 | compute fys interface property/atom fy 97 | compute fzs interface property/atom fz 98 | 99 | ## **************** Sampling data and run 0 ***************** 100 | 101 | fix 1 main nve 102 | 103 | variable N equal "count(all)" 104 | variable NL equal "count(interface_L)" 105 | variable NR equal "count(interface_R)" 106 | 107 | ## ****************** Initialize groups- ******************** 108 | 109 | group atoms_id id 1 110 | 111 | variable hstep equal 0.01 # Amount of displacement 112 | variable hstepm2 equal -2*v_hstep # Negative 113 | 114 | print 'hstepm2 = ${hstepm2}' # Print it if you need 115 | 116 | shell rm ${filetowrite} 117 | 118 | dump helpdump interface custom 1 ${filetowrite} id c_fxs c_fys c_fzs 119 | dump_modify helpdump sort id 120 | dump_modify helpdump append yes 121 | 122 | ## ***************** Write the interface particle id and type to ${filetowrite} **************** 123 | 124 | print "NL ${NL}" append ${filetowrite} 125 | print "NR ${NR}" append ${filetowrite} 126 | 127 | label loop_i 128 | 129 | variable i loop $N 130 | 131 | variable yi equal y[${i}] 132 | variable boolleft equal (y[${i}]<${middle})&&(y[${i}]>=${mid_left}) 133 | variable boolright equal (y[${i}]>${middle})&&(y[${i}]<=${mid_right}) 134 | # print "${i} ${boolleft} ${boolright}" # Uncomment if you need to visualize data 135 | if "${boolleft}" then & 136 | "print '${i} 1' append ${filetowrite}" 137 | if "${boolright}" then & 138 | "print '${i} 2' append ${filetowrite}" 139 | next i 140 | 141 | jump SELF loop_i 142 | 143 | ## ***************** Loop over atoms on one side, compute forces in all others ************* 144 | 145 | print "HSTEP ${hstep}" append ${filetowrite} 146 | thermo_modify flush yes 147 | 148 | variable counter equal 0 ## Define a counter 149 | 150 | ## Next loop function 151 | 152 | label loop_j 153 | 154 | variable j loop $N 155 | 156 | variable yi equal y[${j}] 157 | variable boolleft equal (${yi}<${middle})&&(${yi}>=${mid_left}) 158 | variable boolright equal (${yi}>${middle})&&(${yi}<=${mid_right}) 159 | 160 | # print "${j} ${boolleft} ${boolright}" # Uncomment if you need to visualize data 161 | if "!${boolleft}" then & 162 | "next j" & 163 | "jump SELF loop_j" & 164 | "jump SELF final_break" 165 | group atoms_id delete 166 | group atoms_id id ${j} 167 | 168 | # ********* X-direction displacement to positive and negative direction ********** 169 | 170 | displace_atoms atoms_id move ${hstep} 0 0 171 | variable counter equal ${counter}+1 172 | reset_timestep ${counter} 173 | print "counter=${counter}" 174 | run 0 ## Update the forces in the compute 175 | 176 | displace_atoms atoms_id move ${hstepm2} 0 0 177 | variable counter equal ${counter}+1 178 | reset_timestep ${counter} 179 | print "counter=${counter}" 180 | run 0 ## Update the forces in the compute 181 | 182 | displace_atoms atoms_id move ${hstep} 0 0 183 | 184 | # ********* Y-direction displacement to positive and negative direction ********** 185 | 186 | displace_atoms atoms_id move 0 ${hstep} 0 187 | variable counter equal ${counter}+1 188 | reset_timestep ${counter} 189 | print "counter=${counter}" 190 | run 0 ## Update the forces in the compute 191 | 192 | displace_atoms atoms_id move 0 ${hstepm2} 0 193 | variable counter equal ${counter}+1 194 | reset_timestep ${counter} 195 | print "counter=${counter}" 196 | run 0 ## Update the forces in the compute 197 | 198 | displace_atoms atoms_id move 0 ${hstep} 0 199 | 200 | # ********* Z-direction displacement to positive and negative direction ********** 201 | 202 | displace_atoms atoms_id move 0 0 ${hstep} 203 | variable counter equal ${counter}+1 204 | reset_timestep ${counter} 205 | print "counter=${counter}" 206 | run 0 ## Update the forces in the compute 207 | 208 | displace_atoms atoms_id move 0 0 ${hstepm2} 209 | variable counter equal ${counter}+1 210 | reset_timestep ${counter} 211 | print "counter=${counter}" 212 | run 0 ## Update the forces in the compute 213 | 214 | displace_atoms atoms_id move 0 0 ${hstep} 215 | 216 | next j 217 | jump SELF loop_j 218 | label final_break -------------------------------------------------------------------------------- /lammps_input_files/relax_thermal.in: -------------------------------------------------------------------------------- 1 | ## ***************** Initialization # basis *************** 2 | units metal 3 | dimension 3 4 | boundary p p p 5 | atom_style atomic 6 | atom_modify map hash 7 | # ****************** read data ***************** 8 | read_data onelayer.data 9 | 10 | # mass 11 | # First layer 12 | mass 1 10.811000 # B1 13 | mass 2 12.010700 # C1 14 | mass 3 14.006700 # N1 15 | 16 | # ******************* Define a few parameters ********************** 17 | 18 | variable T equal 300 # average temperature 300K 19 | variable DT equal 0.0005 # timestep 0.5fs (Read from the restart file) 20 | variable T_low equal 270 # Heat sink 270K 21 | variable T_hight equal 330 # Heat source 330K 22 | 23 | variable restartfile string optimize.restart # Write the restart file in preparation for generating the force constant 24 | 25 | # ********************* Potential function setting ***************** 26 | 27 | pair_style tersoff 28 | pair_coeff * * BNC.tersoff B C N 29 | 30 | # ********************* thermo output ************************ 31 | 32 | thermo 1000 33 | thermo_style custom step temp lx ly lz press vol pxx pyy pzz pe ke etotal #energy output 34 | 35 | ## *********************** Initialization ##relaxation< *********************** 36 | ## *********************** Optimize at 0 K *********************** 37 | ## *********************** Static equilibrium ************************** 38 | 39 | dump 1 all custom 1000 dump.minimization id type x y z # Output the minimum structure, see whether the structure is reasonable 40 | dump_modify 1 sort id 41 | 42 | #neighbor 0.3 bin 43 | #neigh_modify once yes ### Generally no Settings are required 44 | 45 | fix 1 all nve 46 | min_style cg 47 | minimize 1.0e-5 1.0e-8 1000000 1000000 48 | undump 1 49 | unfix 1 50 | 51 | # ************************* Set velocity at 300K ********************** 52 | 53 | reset_timestep 0 # Time reset 54 | velocity all create ${T} 619206 mom yes rot yes dist gaussian # Setting Random seed 55 | 56 | # ************************* The following to divide block *********************** 57 | # ************************* For Y direction ************************************** 58 | 59 | variable y_max equal ly 60 | variable P equal ${y_max}/2-100 61 | variable P1 equal ${y_max}/2+100 62 | 63 | variable tmp1 equal ${P1}-${P} 64 | variable tmp equal ${tmp1}/40 65 | 66 | variable L1 equal ${P}+3*${tmp} 67 | variable R1 equal ${P1}-3*${tmp} 68 | 69 | region lfixed block INF INF INF ${P} INF INF units box 70 | region rfixed block INF INF ${P1} INF INF INF units box 71 | 72 | region hot block INF INF ${P} ${L1} INF INF units box 73 | region cold block INF INF ${R1} ${P1} INF INF units box 74 | 75 | region fixed union 2 lfixed rfixed 76 | 77 | region main block INF INF ${P} ${P1} INF INF units box 78 | 79 | region main_nvt block INF INF ${L1} ${R1} INF INF units box 80 | 81 | 82 | group lfixed region lfixed 83 | group rfixed region rfixed 84 | group hot region hot 85 | group cold region cold 86 | 87 | group main region main 88 | group main_nvt region main_nvt 89 | 90 | ## ***************** Frozen atomic group ************** 91 | 92 | group freeze region fixed 93 | 94 | ## ***************** Group layer_1 (Gr) ***************** 95 | 96 | #group Gr type 4 # If you need 97 | 98 | ## ***************** Group layer_2 (Gr_Hbn) ************** 99 | 100 | group Gr_Hbn type 1 2 3 101 | 102 | ##***************** Divide the zone into blocks for extracting the temperature blocks ***************** 103 | 104 | variable average_40 equal (${P1}-${P})/40 105 | variable average_50 equal (${P1}-${P})/50 106 | variable middle equal ${y_max}/2 107 | variable average_1 equal (${middle}-${P})/20 108 | variable average_2 equal (${P1}-${middle})/20 109 | 110 | region main_1 block INF INF ${P} ${middle} INF INF units box 111 | region main_2 block INF INF ${middle} ${P1} INF INF units box 112 | region main_main block INF INF ${P} ${P1} INF INF units box 113 | 114 | group main_1 region main_1 115 | group main_2 region main_2 116 | group main_main region main_main 117 | 118 | ##***************** Velocity groups for transmission calculation ***************** 119 | 120 | variable dmid equal 6 ## Set to 6 (A) here 121 | variable mid_left equal ${middle}-${dmid} 122 | variable mid_right equal ${middle}+${dmid} 123 | 124 | region int_L block INF INF ${mid_left} ${middle} INF INF units box 125 | region int_R block INF INF ${middle} ${mid_right} INF INF units box 126 | 127 | group interface_L region int_L 128 | group interface_R region int_R 129 | group interface union interface_L interface_R 130 | 131 | ## ************** Freeze (Freeze some of the atoms of the model) ************** 132 | 133 | velocity freeze set 0.0 0.0 0.0 units box 134 | fix 3 freeze nve/noforce 135 | 136 | ## *************** Calculate some thermodymanic quantities ******************* 137 | 138 | compute Thot hot temp/region hot 139 | compute Tcold cold temp/region cold 140 | compute Ftemp freeze temp/region fixed 141 | 142 | # **************** Compute temperature ***************** 143 | 144 | compute ALLKe all ke/atom 145 | variable KB equal 8.625e-5 146 | variable TEMP atom c_ALLKe/1.5/${KB} 147 | fix Totaltemperatom all ave/atom 10 50000 500000 v_TEMP 148 | 149 | # **************** Now optimize at 300K ******************** 150 | # **************** The 1nd equilibration run ******************** 151 | 152 | fix 1 main nvt temp ${T} ${T} 0.1 153 | dump 1 all custom 500000 dump.optimize id type x y z f_Totaltemperatom 154 | dump_modify 1 sort id ## Sort each atom 155 | 156 | thermo_style custom step temp lx ly lz c_Thot c_Tcold c_Ftemp press pe ke etotal 157 | thermo 1000 158 | 159 | ## Set the time_step 160 | 161 | timestep ${DT} 162 | 163 | #restart 164 | #restart 500000 optimize.*.restart 165 | 166 | run 3000000 167 | 168 | undump 1 169 | unfix 1 170 | 171 | #minimize 0 1.0e-3 1000 1000 # (optional) 172 | min_style cg 173 | minimize 1.0e-5 1.0e-8 1000000 1000000 174 | 175 | run 0 176 | 177 | write_restart ${restartfile} 178 | 179 | write_data data.pos nocoeff 180 | 181 | variable v1 equal xlo 182 | variable v2 equal xhi 183 | variable v3 equal ylo 184 | variable v4 equal yhi 185 | variable v5 equal zlo 186 | variable v6 equal zhi 187 | print "************** The system boundaries are ****************" 188 | print " X-direction is ---------* ${v1} ${v2} *-----------(A)" 189 | print " Y-direction is ---------* ${v3} ${v4} *-----------(A)" 190 | print " Z-direction is ---------* ${v5} ${v6} *-----------(A)" 191 | 192 | print "*********** You can use the restart file for the 2nd equilibration run (for thermal transport) **************" 193 | print "****************** You can also use the restart file to generate force constant files **************" 194 | 195 | 196 | # ************************ The second stage ********************** 197 | # ************************ The 2nd equilibration run ********************** 198 | # ************************ Write a shell script to generate velocity random number ******************* 199 | 200 | variable hot_velocity equal 611535 201 | variable cold_velocity equal 27117 202 | variable random_seed equal 0.1 ## To get excellent kinetic properties, this is a good choice 203 | 204 | fix 1 main nve 205 | fix Hot hot langevin ${T_hight} ${T_hight} ${random_seed} ${hot_velocity} tally yes 206 | fix Cold cold langevin ${T_low} ${T_low} ${random_seed} ${cold_velocity} tally yes #langevin 207 | 208 | ## Uncomment and use VMD to check that interface definitions are what you expect 209 | 210 | dump 1 all custom 500000 dump.relaxation id type x y z f_Totaltemperatom 211 | dump_modify 1 sort id 212 | 213 | dump 2 main_main custom 500000 dump.main id type x y z f_Totaltemperatom 214 | dump_modify 2 sort id 215 | 216 | dump 3 main_1 custom 500000 dump.hot id type x y z f_Totaltemperatom 217 | dump_modify 3 sort id 218 | 219 | dump 4 main_2 custom 500000 dump.cold id type x y z f_Totaltemperatom 220 | dump_modify 4 sort id 221 | 222 | ## Write interfacial structure to file for Ovito visualization 223 | 224 | dump 5 interface custom 500000 dump.interface id type x y z f_Totaltemperatom 225 | dump_modify 5 sort id 226 | 227 | 228 | variable tdiff equal c_Thot-c_Tcold 229 | 230 | thermo_style custom step temp lx ly lz c_Thot c_Tcold c_Ftemp f_Hot f_Cold v_tdiff 231 | thermo 1000 232 | 233 | run 4000000 234 | 235 | unfix Totaltemperatom 236 | undump 1 237 | undump 2 238 | undump 3 239 | undump 4 240 | undump 5 241 | 242 | # ************************** Collect Velocities for the calculation of force constants ************************* 243 | 244 | variable dn equal 10 245 | 246 | dump vels interface custom ${dn} vels.dat id type vx vy vz 247 | dump_modify vels format line "%d %d %0.8g %0.8g %0.8g" 248 | dump_modify vels sort id 249 | 250 | dump vels_L interface_L custom ${dn} force_vels_left.dat id type fx fy fz vx vy vz 251 | dump_modify vels_L format line "%d %d %0.8g %0.8g %0.8g %0.8g %0.8g %0.8g" 252 | dump_modify vels_L sort id 253 | 254 | dump vels_R interface_R custom ${dn} force_vels_right.dat id type fx fy fz vx vy vz 255 | dump_modify vels_R format line "%d %d %0.8g %0.8g %0.8g %0.8g %0.8g %0.8g" 256 | dump_modify vels_R sort id 257 | 258 | run 500000 259 | 260 | undump vels 261 | undump vels_L 262 | undump vels_R 263 | 264 | # *************************** The third stage ************************ 265 | # **************************** Reset langevin thermostats to zero energy accumulation ****************** 266 | # **************************** Thermal conductivity (NEMD) calculation ************************ 267 | # **************************** Reset time step ************************* 268 | 269 | reset_timestep 0 270 | 271 | # Reset langevin thermostats 272 | 273 | fix Hot hot langevin ${T_hight} ${T_hight} ${random_seed} ${hot_velocity} tally yes 274 | fix Cold cold langevin ${T_low} ${T_low} ${random_seed} ${cold_velocity} tally yes #langevin 275 | 276 | thermo_style custom step temp lx ly lz c_Thot c_Tcold c_Ftemp f_Hot f_Cold v_tdiff 277 | thermo_modify lost warn flush yes 278 | 279 | fix hot1 hot ave/time 10 100 1000 f_Hot file hot.txt 280 | fix cold1 cold ave/time 10 100 1000 f_Cold file cold.txt 281 | 282 | compute BLOCKSZ_40 main_main chunk/atom bin/1d y lower ${average_40} units box 283 | 284 | fix T_PROFILEZ_40 main_main ave/chunk 100 30000 3000000 BLOCKSZ_40 v_TEMP file temp_40.txt 285 | 286 | compute BLOCKSZ_50 main_main chunk/atom bin/1d y lower ${average_50} units box 287 | 288 | fix T_PROFILEZ_50 main_main ave/chunk 100 30000 3000000 BLOCKSZ_50 v_TEMP file temp_50.txt 289 | 290 | compute BLOCKS_1 main_1 chunk/atom bin/1d y lower ${average_1} units box 291 | fix T_PROFILE_1 main_1 ave/chunk 100 30000 3000000 BLOCKS_1 v_TEMP file temp_1.txt 292 | 293 | compute BLOCKSZ_2 main_2 chunk/atom bin/1d y lower ${average_2} units box 294 | 295 | fix T_PROFILEZ_2 main_2 ave/chunk 100 30000 3000000 BLOCKSZ_2 v_TEMP file temp_2.txt 296 | 297 | ## ********************* Run enough time *********************** 298 | 299 | restart 3000000 thermal.*.restart 300 | 301 | run 6000000 302 | -------------------------------------------------------------------------------- /scripts/Makefile: -------------------------------------------------------------------------------- 1 | CC=g++ 2 | CCFlags=-Wall 3 | EXECUTABLE=compactify_vels 4 | 5 | all: 6 | $(CC) $(CCFLAGS) compactify_vels.cpp -o $(EXECUTABLE) 7 | clean: 8 | rm -f compactify_vels 9 | 10 | -------------------------------------------------------------------------------- /scripts/compactify_vels.cpp: -------------------------------------------------------------------------------- 1 | // -*- coding: utf-8 -*- 2 | // Kimmo Sääskilahti, 2015 3 | 4 | // Usage: compactify_vels lammps_dump_file [output_file] 5 | 6 | /* 7 | Program writes the velocity data file produced by LAMMPS 8 | in a more compact, ravelled form without the additional data 9 | appearing for each time step in the dump file. The assumed commands used for dumping the velocities from LAMMPS is as follows: 10 | 11 | dump vels interface custom dt_dump filename.vels.dat id type vx vy vz 12 | dump_modify vels format "%d %d %.8g %.8g %.8g" 13 | dump_modify vels sort id 14 | 15 | "interface" is the group of atoms at the interface where SHC is calculated 16 | "dt_dump" is the sampling time step (integer) specifying the maximum frequency 17 | */ 18 | 19 | #include 20 | #include 21 | #include 22 | #include 23 | using namespace std; 24 | 25 | void skip_lines(istream&,size_t); 26 | 27 | 28 | 29 | int main(int argc,char** argv){ 30 | 31 | 32 | 33 | if(argc==1){ 34 | cout<<"Usage: Give the filenames on the command line."<>filename; 52 | //cout<<"Reading from file "<>filename2; 55 | 56 | cout<<"Writing to file "<>t0; 74 | cout<<"The initial time step is "<> N; 79 | cout<<"The number of atoms is "<>ids[i]; 86 | getline(file1,str); // Skip the rest of the line 87 | //cout<>t1; 91 | cout<<"The difference of time steps is "<::eof()){ // The next character is not EOF 121 | if ((iter)%100000==0) 122 | cout<<"iter="<>id>>type>>vx>>vy>>vz; 133 | //file2< 0: # Not the first chunk 369 | self.NChunks = k - 1 370 | break 371 | else: 372 | exitFlag = True 373 | self.oms_fft = np.fft.rfftfreq(self.chunkSize, d=self.sampleTimestep) * 2 * np.pi 374 | Nfreqs = np.size(self.oms_fft) 375 | print("Changing chunk size to " + str(int(np.size(velArray) / NDOF)) + "!") 376 | 377 | # Reshape the array so that each row corresponds to different degree of freedom (e.g. particle 1, direction x, y, z etc.) 378 | 379 | velArray = np.reshape(velArray, (NDOF, self.chunkSize), order='F') # Write in column order 380 | 381 | # FFT with respect to the second axis (NOTE THE USE OF RFFT) 382 | velFFT = np.fft.rfft(velArray, axis=1) # axis = 0 for rows, axis = 1 for column 383 | velFFT *= self.sampleTimestep 384 | 385 | self.velsL = np.zeros((3 * self.NL, Nfreqs), dtype = np.complex128) 386 | self.velsR = np.zeros((3 * self.NR, Nfreqs), dtype = np.complex128) 387 | 388 | ## Atoms on the left (self.ids_L is the left interfacial atom indices) 389 | 390 | self.velsL[0::3, :] = velFFT[3 * self.ids_L, :] # X-direction velocity 391 | self.velsL[1::3, :] = velFFT[3 * self.ids_L + 1, :] # Y-direction velocity 392 | self.velsL[2::3, :] = velFFT[3 * self.ids_L + 2, :] # Z-direction velocity 393 | 394 | ## Atoms on the right (self.ids_L is the right interfacial atom indices) 395 | 396 | self.velsR[0::3, :] = velFFT[3 * self.ids_R, :] # X-direction velocity 397 | self.velsR[1::3, :] = velFFT[3 * self.ids_R + 1, :] # Y-direction velocity 398 | self.velsR[2::3, :] = velFFT[3 * self.ids_R + 2, :] # Z-direction velocity 399 | 400 | ## For different direction spectral SHC: 401 | if self.in_plane or self.out_of_plane: 402 | 403 | self._differ_direction() 404 | 405 | # Spectral heat current for the specific chunk 406 | SHC = np.zeros(Nfreqs) 407 | 408 | ''' 409 | In formula programming, the SHC here is already the sum of the left and right interface atoms 410 | ''' 411 | for ki in range(1, Nfreqs): # Skip the first one with zero frequency 412 | SHC[ki] = -2.0 * np.imag(np.dot(self.velsL[:, ki], np.dot(self.Kij, np.conj(self.velsR[:, ki])))) / self.oms_fft[ki] # np.dot is the matrix product 413 | 414 | # Normalize correctly 415 | 416 | SHC /= (self.chunkSize * self.sampleTimestep) 417 | 418 | # Change units 419 | 420 | SHC *= self.scaleFactor 421 | 422 | # Copy the SHC value before modifying it 423 | 424 | SHC_orig = SHC.copy() 425 | 426 | # Smooth the value 427 | 428 | df = (self.oms_fft[1] - self.oms_fft[0]) / (2 * np.pi) # Angular frequency, positive val (w is the angular frequency) 429 | SHC = self._smoothen(SHC, df, self.widthWin) 430 | 431 | # Time average 432 | if not exitFlag: # If Nfreqs has changed, the running averaging cannot be performed 433 | self.SHC_smooth = (k * self.SHC_smooth + SHC) / (k + 1.0) 434 | # The square 435 | self.SHC_smooth2 = (k * self.SHC_smooth2 + SHC ** 2) / (k + 1.0) 436 | # The non-smoothened average 437 | self.SHC_average = (k * self.SHC_average + SHC_orig) / (k + 1.0) 438 | if self.backupPrefix is not None: 439 | np.save(self.backupPrefix + '_backup_oms.npy', self.oms_fft) 440 | np.save(self.backupPrefix + '_backup_SHC.npy', self.SHC_smooth) 441 | import cPickle as pickle 442 | with open(self.backupPrefix + '_run_PP.pckl', 'w') as pf: 443 | pickle.dump(self, pf) 444 | elif exitFlag and k == 0: # First chunk and new chunk size, needs re-initializing the vectors as Nfreqs may have changed 445 | self.SHC_smooth = SHC 446 | self.SHC_smooth2 = SHC ** 2 447 | self.SHC_average = SHC_orig 448 | self.NChunks = 1 449 | break 450 | else: # This should never be reached 451 | assert False, "SHCPostProc should not reach here (exitFlag=True and k>0)." 452 | 453 | # Calculate the error estimate at each frequency from the between-chunk variances 454 | 455 | if self.NChunks > 1: 456 | print("\nCalculating error estimates.") 457 | samplevar = (self.NChunks / (self.NChunks - 1.0)) * (self.SHC_smooth2 - self.SHC_smooth ** 2) 458 | self.SHC_error = np.sqrt(samplevar) / np.sqrt(self.NChunks) 459 | else: 460 | self.SHC_error = None 461 | 462 | print("\nFinished post-processing.") 463 | 464 | self._toc() 465 | 466 | 467 | if __name__ == "__main__": 468 | 469 | fileprefix = 'Fij.dat' 470 | in_file = 'forces.in' ## The in file for lammps 471 | atomic_velocities_file = 'vels.dat' 472 | compact_velocities_file = 'vels.compact.dat' 473 | frequency_window_width = 2e12 ## Hz 474 | 475 | #*************** eV/ps^2; 1 eV = 1.602e-19 J, 1 ps = 1e-12 s *************** 476 | unit_scaling_factor = 1.602e-19 / 1e-20 * 1e4 ## convert: v*dF/du*v = [A/ps]*[eV/A]/[A]*[A/ps] 477 | 478 | md_timestep = 0.5e-15 ## second 479 | area = 62.119 * 3.35 ## A^2, it depends on your case 480 | Tem_jump = 60 ## 60K is the temperature jump 481 | Kb = 1.380649e-23 ## Boltzmann's constant, J/K 482 | 483 | postprocessor = SHCPostProc(compact_velocities_file, 484 | fileprefix, 485 | dt_md = md_timestep, 486 | scaleFactor = unit_scaling_factor, 487 | LAMMPSDumpFile = atomic_velocities_file, 488 | widthWin = frequency_window_width, 489 | LAMMPSInFile = in_file, 490 | in_plane = False, 491 | out_of_plane = False, 492 | reCalcVels = True, 493 | reCalcFC = True) 494 | 495 | postprocessor.postProcess() 496 | 497 | # Plotting if available 498 | 499 | import matplotlib.pylab as plt 500 | import scipy.integrate as sci # For calculate the area 501 | 502 | # Unit conversion 503 | x_Frequency = postprocessor.oms_fft/(2*np.pi*1.0e12) # Conversion from Hz to THz 504 | 505 | # The unit of heat currents is Joule (J), which is W / Hz 506 | # Calculate the Spectral thermal conductance 507 | y_ITC = postprocessor.SHC_smooth / (1.0e-12 * area * 1.0e-20 * Tem_jump * 1.0e9) # From W to GW (/1.0e9) 508 | 509 | # Calculate the phonon transmission T(w) 510 | T_w = postprocessor.SHC_smooth / (Kb * Tem_jump) # Dimensionless 511 | 512 | # Calculate the accumulated thermal conductance 513 | Freq_number = len(x_Frequency) 514 | accumulated_ITC = [] 515 | accumulated_count = 0 516 | 517 | for i in range(Freq_number): 518 | accumulated_count = sci.trapz(y_ITC[0:i], x_Frequency[0:i]) 519 | accumulated_ITC.append(accumulated_count) 520 | 521 | print('\nThe accumulated thermal conductance is ' + str(accumulated_count) + ' (GW/m^2/K)') 522 | 523 | # Save the frequencies and smoothened spectral heat currents to text file 524 | np.savetxt('frequencies_and_ITC.txt', np.column_stack((x_Frequency, y_ITC))) 525 | np.savetxt('frequencies_accumulated_ITC.txt', np.column_stack((x_Frequency, accumulated_ITC))) 526 | 527 | 528 | # *************************** Plotting ************************* (It can be reduced to a graph function) 529 | # Phonon transmission T(w) 530 | plt.plot(x_Frequency, T_w, '-', linewidth=3, label="Interfacial Phonon Transmission") 531 | plt.xlabel('w/(2*pi) (THz)') 532 | plt.ylabel('Transmission') 533 | plt.xlim(0, max(x_Frequency)) # Frequency range 534 | plt.ylim(0, max(T_w) + 5) # It depends on your case 535 | plt.legend(fontsize=15, loc='best') 536 | plt.show() 537 | plt.savefig(fileprefix+'_Tw.eps') 538 | 539 | # Spectral thermal conductance 540 | plt.plot(x_Frequency, y_ITC, '-', linewidth=3, label="Spectral thermal conductance") 541 | plt.xlabel('w/(2*pi) (THz)') 542 | plt.ylabel('G(w) (GW/m^2/K/THz)') 543 | plt.xlim(0, max(x_Frequency)) # Frequency range 544 | plt.ylim(0, max(y_ITC)+(max(y_ITC)/2)) # It depends on your case 545 | print('\nThe total thermal conductance is ' + str(sci.trapz(y_ITC, x_Frequency)) + ' (GW/m^2/K)\n') 546 | plt.legend(fontsize=15, loc='best') 547 | plt.show() 548 | plt.savefig(fileprefix+'_SHC.eps') 549 | 550 | # Spectral accumulated thermal conductance 551 | plt.plot(x_Frequency, accumulated_ITC, 'or', label="Accumulated thermal conductance") 552 | plt.xlabel('w/(2*pi) (THz)') 553 | plt.ylabel('G(w) (GW/m^2/K)') 554 | plt.xlim(0, max(x_Frequency)) # Frequency range 555 | plt.ylim(0, accumulated_count + 1) # It depends on your case 556 | plt.legend(fontsize=15, loc='best') 557 | plt.show() 558 | plt.savefig(fileprefix+'_accumulated_ITC.eps') -------------------------------------------------------------------------------- /sdhc/__init__.py: -------------------------------------------------------------------------------- 1 | from . import SHC_generate as SHCPostProcModule 2 | from .SHC_generate import * 3 | from . import force_calculate as fcCalcModule 4 | from .force_calculate import * 5 | 6 | __all__ = ["__version__"] + fcCalcModule.__all__ + SHCPostProcModule.__all__ 7 | 8 | del fcCalcModule 9 | del SHCPostProcModule -------------------------------------------------------------------------------- /sdhc/__main__.py: -------------------------------------------------------------------------------- 1 | from .SHC_generate import * 2 | from .force_calculate import * 3 | 4 | 5 | def main(): 6 | print("Not done yet!") 7 | 8 | 9 | if __name__ == '__main__': 10 | main() -------------------------------------------------------------------------------- /sdhc/__version__.py: -------------------------------------------------------------------------------- 1 | __version__ = '0.2.0' -------------------------------------------------------------------------------- /sdhc/force_calculate.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | # -*- coding: utf-8 -*- 3 | 4 | """ 5 | @author: Kimmo Sääskilahti 6 | ksaaskil@gmail.com 7 | 8 | Made some modifications by Liang Ting 9 | liangting.zj@gmail.com 10 | 2020/2/7 14:22:15 11 | """ 12 | 13 | import numpy as np 14 | import sys 15 | 16 | __all__ = ["fcCalc"] 17 | 18 | class fcCalc(object): 19 | """ 20 | Class for computing force constants between atoms. 21 | Uses the `Python library interface `_ 22 | of LAMMPS so you need to have (1) `lammps` in your `PYTHONPATH` and 23 | (2) `liblammps.so` available for the Python package. 24 | :param fileprefix: File prefix (TODO What is this) 25 | :type fileprefix: str 26 | :param restartfile: LAMMPS restart file (The restart file is also required, but here not as an attribute) 27 | :type restartfile: str 28 | """ 29 | def __init__(self, fileprefix): 30 | 31 | self.fileprefix = fileprefix 32 | self.Kij = None 33 | self.inds_left = None ## Used to find the index of the atoms on the left 34 | self.inds_right = None ## Used to find the index of the atoms on the right 35 | self.inds_interface = None ## Used to compare with the atomic index in the dump_velovity file 36 | self.ids_L = None ## Used to index the speed ordinal (left) 37 | self.ids_R = None ## Used to index the speed ordinal (right) 38 | self.natoms = None 39 | self.lmp = None ## Python-Lammps interface 40 | 41 | def __enter__(self): 42 | return self 43 | 44 | def __exit__(self, exc_type, exc_val, exc_tb): 45 | return False 46 | 47 | def preparelammps(self, in_lammps = None, w_interface = 6.0, show_log = False): 48 | """ 49 | Prepare the LAMMPS object for computing force constants. 50 | :param fileprefix: File prefix (lammps in_file) 51 | :type fileprefix: str 52 | :param w_interface: Width of the area of atoms to include in the interface, defaults to 6.0 53 | :type w_interface: float, optional 54 | :param show_log: Whether to write the log file to the generate_force.log file, if true, no log file will be generated. (default False) 55 | :type show_log: boolean, optional 56 | :return: None 57 | """ 58 | from lammps import lammps 59 | 60 | cmd_list = ['-log', 'generate_force.log', '-screen', 'none'] 61 | 62 | if not show_log: 63 | cmd_list += ['-echo', 'none'] 64 | 65 | self.lmp = lammps(cmdargs = cmd_list) 66 | 67 | if in_lammps is not None: 68 | pass 69 | else: 70 | sys.exit('\n\tFile error: The in file that lammps needs to read does not exist!\n') 71 | 72 | #lines = open(in_lammps,'r').readlines() 73 | #for line in lines: self.lmp.command(line) 74 | """ 75 | Do the same as lmp.command(filename) but don't allow the script to be 76 | continued after quit. 77 | """ 78 | lines = open(in_lammps,'r').readlines() 79 | for line in lines: 80 | #print(line) 81 | if "quit" in line and line[0] != "#": 82 | sys.exit('\n\tQuit error: It is not appropriate ' 83 | 'to exit the execution of the in.file at this time\n') ## Quit lammps if find the keyword 'quit' 84 | else: 85 | self.lmp.command(line) 86 | 87 | # Get the position of the interface, at the middle by default (0.5) 88 | 89 | ylo = self.lmp.extract_global("boxylo", 1) 90 | yhi = self.lmp.extract_global("boxyhi", 1) 91 | #print "Box is [%f,%f]." % (ylo, yhi) # Print the boundaries of the box (optional) 92 | 93 | # These variables (including middle, mid_left, and mid_right) must be predefined in the in_file 94 | middle = self.lmp.extract_variable("middle", "all", 0) 95 | mid_left = self.lmp.extract_variable("mid_left", "all", 0) 96 | mid_right = self.lmp.extract_variable("mid_right", "all", 0) # group = group ID ('all') (ignored for equal-style variables) 97 | w_interface_infile = (mid_right - mid_left)/2 98 | 99 | if (w_interface_infile != w_interface): 100 | sys.exit('\n\t Parameter setting ERROR: The settings for w_interface do ' 101 | 'not match those in lammps\n') 102 | 103 | # Coordinates ordered by atom ID 104 | coords_data = self.lmp.gather_atoms("x", 1, 3) 105 | 106 | # Coordinates in a numpy array 107 | coords = np.array(coords_data[:], dtype=np.dtype('f8')) 108 | self.natoms = self.lmp.extract_global("natoms", 0) 109 | 110 | ''' Data structures after rashape 111 | 112 | atom1_x (coords_data[0]) atom1_y (coords_data[1]) atom1_z (coords_data[2]) 113 | atom2_x (coords_data[3]) atom2_y (coords_data[4]) atom2_z (coords_data[5]) 114 | ''' 115 | coords = np.reshape(coords, (self.natoms, 3)) 116 | 117 | # Y-coordinates in a Numpy array 118 | ys = coords[:, 1] ## xs=coords[:, 0] , ys = coords[:, 1], zs = coords[:, 2] 119 | 120 | ''' 121 | (1) minimize 0 1.0e-3 1000 1000 # (after relaxing the structures to the potential minimum) 122 | run 0 123 | After the structure is completely relaxed, the process of energy minimization must be added 124 | 125 | (2) Since energy minimization may result in different atomic Numbers on the left and right sides of the interface, 126 | the definition of the width of the interface can be fine-tuned. 127 | 128 | (3) The program will automatically identify if the left and right atom ids are the same as the atom id of the dump_velcity_file. 129 | ''' 130 | # Atom on the left side? 131 | mask_left = np.logical_and(ys < middle, ys >= mid_left-1) ## return boolean 132 | # Atom on the right side? 133 | mask_right = np.logical_and(ys > middle, ys <= mid_right) 134 | 135 | # Note that these indices differ from atom IDs by a factor of one 136 | 137 | self.inds_left = np.where(mask_left)[0] 138 | self.inds_right = np.where(mask_right)[0] 139 | 140 | # All atom indices sorted by atom ID, duplicates removed 141 | # Note that these indices differ from atom IDs by a factor of one 142 | 143 | self.inds_interface = np.unique(np.concatenate((self.inds_left, self.inds_right))) 144 | 145 | # Where are the atoms of the left atom set 146 | 147 | self.ids_L = np.in1d(self.inds_interface, self.inds_left) # To find the subset 148 | self.ids_L = np.where(self.ids_L)[0] # or np.where(np.in1d(aArray,bArray))[0] 149 | 150 | # Atoms of the right set 151 | 152 | self.ids_R = np.in1d(self.inds_interface, self.inds_right) 153 | self.ids_R = np.where(self.ids_R)[0] 154 | 155 | # Get information from the in file 156 | 157 | N = self.lmp.extract_variable("N", "all", 0) 158 | NL = self.lmp.extract_variable("NL", "all", 0) 159 | NR = self.lmp.extract_variable("NR", "all", 0) 160 | 161 | # Determine whether the number of left and right atoms is equal 162 | 163 | if (len(self.ids_L) != len(self.ids_R) or len(self.ids_L) != NR or len(self.ids_R) != NL): 164 | sys.exit('\n\tLAMMPS SETUP ERROR: Number of atoms on left and right side don\'t match! ' 165 | 'Checking the width definition of the interface is an good option.\n') 166 | 167 | def fcCalc(self, hstep): 168 | """ 169 | Compute force constants and store to `self.Kij`. 170 | :param hstep: Step to use in finite differences (the finite displacement method) 171 | :type hstep: float 172 | :return: None 173 | 174 | This function reads in the [dFi/duj] force constanst from 175 | LAMMPS compute commands. The structure of the infile should be blocks 176 | of data that are N atoms long. Here, N means the number of atoms in 177 | the interface region. Each atom of the N atoms in the block 178 | is the 'i' index in d^2Fi/duj. The Python_LAMMPS code loops over all atoms j 179 | on the left side of the interface; j in the dFi/duj expression. There 180 | are NL = NR atoms on the left side of the inteface, i.e. the number on 181 | each side should (and MUST) be the same. Each atom on the left side, j, is 182 | looped over; in each loop iteration the atom is moved in the +x, then -x, 183 | then back to equilibrium. Then the atom is moved in the +y, then -y, then 184 | back to equilibrium. Finally, the atom is moved in the +z, then -z, then 185 | back to equilibrium. 186 | 187 | Thus, each line in each block in the file corresponds to an atom i. 188 | Each element in each line is the force felt by the atom in the x, y, and 189 | z direction (the force vector elements). For each block, the atom j is 190 | moved iteratively in the +x, then-x, then +y ... etc. 191 | 192 | The function returns kij, the matrix elements of the force constants 193 | between atoms on either side of the interface. 194 | kij has the shape [3*nr,3*nl] -> [dFi-x,y,z,duj-x,y,z]. Each individual 195 | force constant is defined as: 196 | 197 | dFi_a 198 | ---------- 199 | drj_b 200 | 201 | Which is interpreted as the change in force on atom i in the direction 202 | a = (x,y,z) due to the movement of atom j in b=(x,y,z). 203 | Each element of first dimension of the kij matrix corresponds to the 204 | force on atom i due to the movement of atom j in each direction 205 | 206 | dF1_x dF1_x dF1_x dF1_x 207 | ---------- ---------- ---------- ---------- ..... 208 | dr1_x dr1_y dr1_z dr2_x 209 | 210 | 211 | dF1_y dF1_y dF1_y dF1_y 212 | ---------- ---------- ---------- ---------- ..... 213 | dr1_x dr1_y dr1_z dr2_x 214 | 215 | 216 | dF1_z dF1_z dF1_z dF1_z 217 | ---------- ---------- ---------- ---------- ..... 218 | dr1_x dr1_y dr1_z dr2_x 219 | 220 | 221 | dF2_x dF2_x dF2_x dF2_x 222 | ---------- ---------- ---------- ---------- ..... 223 | dr1_x dr1_y dr1_z dr2_x 224 | 225 | : : : : 226 | : : : : 227 | """ 228 | lmp = self.lmp 229 | natoms = self.natoms 230 | inds_left = self.inds_left 231 | inds_right = self.inds_right 232 | 233 | # One-dimensional indices of the atoms on the right side (Y-coordinates) 234 | 235 | inds_right_1d = np.concatenate((3 * inds_right, 3 * inds_right + 1, 3 * inds_right + 2)) 236 | inds_right_1d = np.sort(inds_right_1d) 237 | 238 | Kij = np.zeros((len(inds_left) * 3, len(inds_right) * 3)) 239 | 240 | # Loop over the atoms on the left side 241 | 242 | print ('\nNow start the loop and move the atoms to calculate the force constant!!!') 243 | for i1 in range(0, len(inds_left)): 244 | # (For test) for i1 in range(0,10): 245 | # Index of the atom on the left 246 | ind1 = inds_left[i1] 247 | # Find the indices of atom ind1 in the 1D array (For test) 248 | indx = 3 * ind1 # directions x 249 | indy = 3 * ind1 + 1 # directions y 250 | indz = 3 * ind1 + 2 # directions z 251 | 252 | print "\tMoving atom %i/%i." % (i1 + 1, len(inds_left)) 253 | 254 | # Move atom to directions x(0), y(1), and z(2) 255 | 256 | for direction in [0, 1, 2]: 257 | # Index of the displaced degree of freedom 258 | index = 3 * ind1 + direction 259 | # Get the coordinates from LAMMPS 260 | yc = lmp.gather_atoms("x", 1, 3) 261 | # Move the atom 262 | yc[index] += hstep 263 | # Communicate to LAMMPS 264 | lmp.scatter_atoms("x", 1, 3, yc) 265 | # Run LAMMPS to update the forces 266 | lmp.command("run 0 post no") ## The 'post no' means the full timing summary is skipped; only a one-line summary timing is printed 267 | # Gather the forces 268 | fc1 = lmp.gather_atoms("f", 1, 3) ## The force (including x, y, z) on all the atoms in the interface group 269 | # print "1=",fc1[0] 270 | # print type(fc1) 271 | fc1 = np.array(fc1, dtype=np.dtype('f8')) 272 | # print "2=",fc1[0] 273 | # print fc1[index] ## Print the force of the current atom (if you need to check) 274 | # Move to negative direction 275 | yc[index] -= 2 * hstep 276 | lmp.scatter_atoms("x", 1, 3, yc) 277 | lmp.command("run 0 post no") 278 | fc2 = lmp.gather_atoms("f", 1, 3) 279 | fc2 = np.array(fc2, dtype=np.dtype('f8')) 280 | 281 | # print fc2[index] ## Print the force (negative direction) of the current atom (if you need to check) 282 | # Fill one row of spring constant matrix 283 | 284 | ''' 285 | Calculate the force on all atoms in 286 | the right group due to the current atom's displacement (on the left) 287 | ''' 288 | 289 | Kij[3 * i1 + direction, :] = (fc2[inds_right_1d] - fc1[inds_right_1d]) / (2.0 * hstep) ## fc2 - fc1 (Yes) ---- (Negative-Positive) 290 | yc[index] += hstep 291 | lmp.scatter_atoms("x", 1, 3, yc) ## Back to equilibrium. 292 | 293 | self.Kij = Kij 294 | lmp.close() 295 | 296 | def writeToFile(self): 297 | ''' 298 | Write `self.Kij` to files starting with `self.fileprefix`. 299 | :return: None 300 | ''' 301 | np.save(self.fileprefix + '.Kij.npy', self.Kij) 302 | np.save(self.fileprefix + '.ids_L.npy', self.ids_L) 303 | np.save(self.fileprefix + '.ids_R.npy', self.ids_R) 304 | np.save(self.fileprefix + '.ids_Interface.npy', self.inds_interface) 305 | np.savetxt(self.fileprefix, self.Kij, delimiter=' ') 306 | print('\nKij have been written to the ' + self.fileprefix + ' file\n') 307 | 308 | 309 | if __name__ == "__main__": 310 | 311 | # import argparse 312 | # parser=argparse.ArgumentParser() 313 | # parser.add_argument("filePrefix",help="The prefix of file for which to calculate the force constants") 314 | # parser.add_argument("hstep",default=0.01,help="The displacement used in the finite-difference evaluation of force constants.") 315 | 316 | # args=parser.parse_args() 317 | # fileprefix=args.filePrefix 318 | # hstep=args.hstep 319 | 320 | fileprefix = 'Fij.dat' 321 | hstep = 0.01 ## Maybe hstep = 0.01 is a good choice 322 | in_file = 'forces.in' ## The in file for lammps 323 | 324 | with fcCalc(fileprefix) as fc: 325 | fc.preparelammps(in_lammps = in_file, w_interface = 6.0) 326 | fc.fcCalc(hstep) 327 | fc.writeToFile() 328 | print('Forces Calculate All Done\n') 329 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import find_packages, setup, Command 2 | import stat 3 | import os 4 | from shutil import rmtree 5 | import sys 6 | 7 | # Package meta-data. 8 | NAME = 'sdhc' 9 | DESCRIPTION = 'Tools for computing spectral heat current distribution using LAMMPS NEMD simulations' 10 | URL = 'https://github.com/Tingliangstu/Spectral-decomposition-python-tools' 11 | EMAIL = 'ksaaskil@gmail.com and liangting.zj@gmail.com' 12 | AUTHOR = 'Kimmo S\"a\"askilahti and modify by Liang Ting' 13 | REQUIRES_PYTHON = '>=2.7.8' 14 | SRC_DIR = 'sdhc' # Relative location wrt setup.py 15 | 16 | # Required packages. 17 | REQUIRED = ['numpy'] 18 | 19 | DEV = ['pytest', 'sphinx', 'sphinx_rtd_theme'] 20 | 21 | EXTRAS = {'dev': DEV } 22 | 23 | # Entry point for CLI (relative to setup.py) 24 | ENTRY_POINTS = ['sdhc = sdhc.__main__:main'] 25 | 26 | here = os.path.abspath(os.path.dirname(__file__)) 27 | 28 | # Import the README and use it as the long-description. 29 | with open(os.path.join(here, 'README.md')) as f: 30 | long_description = '\n' + f.read() 31 | 32 | # Load the package's __version__.py module as a dictionary. 33 | about = dict() 34 | with open(os.path.join(here, SRC_DIR, '__version__.py')) as f: 35 | exec(f.read(), about) 36 | 37 | class SetupCommand(Command): 38 | """Base class for setup.py commands with no arguments""" 39 | user_options = [] 40 | 41 | def initialize_options(self): 42 | pass 43 | 44 | def finalize_options(self): 45 | pass 46 | 47 | @staticmethod 48 | def status(s): 49 | """Prints things in bold.""" 50 | print('\033[1m{0}\033[0m'.format(s)) 51 | 52 | def rmdir_if_exists(self, directory): 53 | self.status("Deleting {}".format(directory)) 54 | rmtree(directory, ignore_errors=True) 55 | 56 | 57 | class BuildDistCommand(SetupCommand): 58 | """Support setup.py upload.""" 59 | description = "Build the package." 60 | 61 | def run(self): 62 | 63 | self.status("Removing previous builds...") 64 | self.rmdir_if_exists(os.path.join(here, 'dist')) 65 | 66 | self.status("Building Source and Wheel (universal) distribution...") 67 | os.system("{executable} setup.py sdist bdist_wheel --universal".format(executable=sys.executable)) 68 | sys.exit() 69 | 70 | 71 | def build_docs(): 72 | os.chdir("docs") 73 | os.system("sphinx-apidoc -f -e -o source/ ../sdhc/") 74 | os.system("sphinx-build -M html -D version={version} source build".format(version=about['__version__'])) 75 | 76 | 77 | class BuildDocumentationCommand(SetupCommand): 78 | """Builds the sphinx documentation""" 79 | description = "Builds the sphinx documentation." 80 | 81 | def run(self): 82 | self.status("Removing previous builds...") 83 | 84 | build_dir = os.path.join(here, 'docs/build') 85 | self.rmdir_if_exists(build_dir) 86 | 87 | version_dir = os.path.join(here, 'docs', 'version={version}'.format(version=about['__version__'])) 88 | self.rmdir_if_exists(version_dir) # Need to delete this before building HTML docs 89 | 90 | self.status("Building documentation...") 91 | build_docs() 92 | 93 | self.status("Docs were built to `docs/build`.") 94 | sys.exit() 95 | 96 | 97 | class TestCommand(SetupCommand): 98 | """Support setup.py test.""" 99 | description = "Run local test if they exist" 100 | 101 | def run(self): 102 | os.system("pytest") 103 | sys.exit() 104 | 105 | 106 | setup( 107 | name=NAME, 108 | version=about['__version__'], 109 | description=DESCRIPTION, 110 | long_description=long_description, 111 | long_description_content_type='text/markdown', 112 | author=AUTHOR, 113 | author_email=EMAIL, 114 | python_requires=REQUIRES_PYTHON, 115 | url=URL, 116 | packages=find_packages(exclude=('tests',)), 117 | install_requires=REQUIRED, 118 | extras_require=EXTRAS, 119 | include_package_data=True, 120 | license='Apache 2.0', 121 | classifiers=[ 122 | 'Development Status :: 2 - Pre-Alpha', 123 | 'License :: OSI Approved :: Apache Software License', 124 | 'Programming Language :: Python', 125 | 'Programming Language :: Python :: 2.7', 126 | 'Programming Language :: Python :: 3', 127 | 'Programming Language :: Python :: 3.6', 128 | 'Programming Language :: Python :: 3.7', 129 | 'Operating System :: MacOS', 130 | 'Operating System :: POSIX', 131 | 'Operating System :: Unix' 132 | ], 133 | entry_points={'console_scripts': ENTRY_POINTS}, 134 | cmdclass={'dist': BuildDistCommand, 135 | 'test': TestCommand, 136 | 'doc': BuildDocumentationCommand} 137 | ) --------------------------------------------------------------------------------